added the option to save the DihedralAnalysis results DataFrame as cs…

…v files in provided parent directory

mdpow/analysis/automation/dihedral/automated_dihedral_analysis.py

@@ -155,6 +155,49 @@ def dihedral_groups_ensemble(bonds, datadir,
 
     return df
 
+def save_df(df, df_save_dir=None, resname=None, molname=None):
+    '''Takes a Pandas DataFrame of results from DihedralAnalysis
+       as input before padding the angles to optionaly save the raw
+       data before plotting dihedral angle frequencies as KDE violins
+       with dihedral_violins(). Given a parent directory, creates subdirectory
+       for molecule, saves fully sampled csv and per dihedral atom group selection.
+       
+       :arguments:
+       
+       *df : Pandas DataFrame*
+           results DataFrame from DihedralAnalysis
+           
+       :keywords:
+       
+       *df_save_dir : string*
+           path to parent directory to create
+           subdirectory for saving the csv files
+           
+    '''
+
+    if molname is None:
+        molname = resname
+
+    if df_save_dir is not None:
+        subdir = molname
+        newdir = os.path.join(df_save_dir, subdir)
+        os.mkdir(newdir)
+
+    df = df.sort_values(by=["selection",
+                            "solvent",
+                            "interaction",
+                            "lambda"]).reset_index(drop=True)
+
+    section = df.groupby(by='selection')
+
+    if df_save_dir is not None:
+        df.to_csv(f'{newdir}/{molname}_full_df.csv', index=False)
+        for name in section:
+            sliced_df = df.loc[df['selection'] == name[0]]
+            sliced_df.to_csv(f'{newdir}/{molname}_{name[0]}_df.csv', index=False)
+
+    return
+
 def periodic_angle(df, padding=45):
     '''Takes a Pandas DataFrame of results from DihedralAnalysis
        as input and pads the angles to maintain periodicity
@@ -274,7 +317,7 @@ def plot_violins(df, resname, figdir=None, molname=None, width=0.9):
 
     return plot
 
-def automated_dihedral_analysis(datadir=None, figdir=None,
+def automated_dihedral_analysis(datadir=None, df_save_dir=None, figdir=None,
                                 resname=None, molname=None,
                                 dataframe=None, padding=45, width=0.9,
                                 solvents=('water','octanol'),
@@ -292,6 +335,9 @@ def automated_dihedral_analysis(datadir=None, figdir=None,
        *datadir : string*
            path to the location of MDPOW project data
            
+       *df_save_dir : string*
+           path to the location to save results DataFrame
+           
        *figdir : string*
            optional, path to an existing directory where plots
            can be saved for each dihedral atom group
@@ -352,6 +398,9 @@ def automated_dihedral_analysis(datadir=None, figdir=None,
     else:
         df = dataframe
 
+    if df_save_dir is not None:
+        save_df(df, df_save_dir=df_save_dir, resname=resname, molname=molname)
+
     df_aug = periodic_angle(df, padding=padding)
 
     return plot_violins(df_aug, resname=resname, figdir=figdir, molname=molname, width=width)          

mdpow/analysis/automation/dihedral/directory_iteration.py

@@ -7,7 +7,7 @@
 
 
 
-def directory_iteration(directory_paths, figdir=None, padding=45, width=0.9,
+def directory_iteration(directory_paths, df_save_dir=None, figdir=None, padding=45, width=0.9,
                         solvents=('water','octanol'), interactions=('Coulomb','VDW'),
                         start=None, stop=None, step=None):
     '''Takes a Pandas DataFrame created by directory_paths as input
@@ -24,6 +24,9 @@ def directory_iteration(directory_paths, figdir=None, padding=45, width=0.9,
         optional, path to existing directory where plots
         can be saved for each MDPOW project analyzed
         
+    *df_save_dir : string*
+           path to the location to save results DataFrame
+        
     *padding : int*
         must be in degrees, values for angle padding function
         used for KDE violin plots of dihedral angle frequencies
@@ -60,7 +63,7 @@ def directory_iteration(directory_paths, figdir=None, padding=45, width=0.9,
             resname = row.resname
             datadir = row.path
 
-            ada.automated_dihedral_analysis(datadir=datadir, figdir=figdir,
+            ada.automated_dihedral_analysis(datadir=datadir, df_save_dir=df_save_dir, figdir=figdir,
                                             molname=molname, resname=resname,
                                             padding=padding, width=width,
                                             solvents=solvents, interactions=interactions,